The 21-year-old Sharma, in his fourth year as a pro, have five wins on the Indian domestic Tour, including one six weeks ago, but he has never finished better than third on either Asian or European Tour.
He was second in an Asian Development Tour event in 2015.
Playing just his 10th European Tour event and still looking for his first international pro win, Sharma also became the first player to be 20 under or better after 54 holes on the European Tour since Rory McIlroy at the 2015 Omega Dubai Desert Classic.
"I'm really happy," Shubhankar said. "I wanted to play even though I shot a 10 under yesterday and it is always difficult to follow up on a low round. I'm really proud of the way I played today.
"I'm very pleased that I came to Joburg Open. I had my visa but it has been a very long season, so was contemplating if I wanted to come here. I'm really happy that I did!"
Swede Christofer Blomstrand raised hopes of a 59 on his 26th birthday but had to settle for a 62 to sit 15 under and five shots behind leader Sharma.
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